/*
 * Copyright 2006-2018 The MZmine 2 Development Team
 *
 * This file is part of MZmine 2.
 *
 * MZmine 2 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 *
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with MZmine 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

/*
 * Code created was by or on behalf of Syngenta and is released under the open source license in use
 * for the pre-existing code or project. Syngenta does not assert ownership or copyright any over
 * pre-existing work.
 */

package net.sf.mzmine.modules.peaklistmethods.identification.nist;

import java.util.Collection;

import javax.annotation.Nonnull;

import net.sf.mzmine.datamodel.MZmineProject;
import net.sf.mzmine.datamodel.PeakList;
import net.sf.mzmine.datamodel.PeakListRow;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.modules.MZmineModuleCategory;
import net.sf.mzmine.modules.MZmineProcessingModule;
import net.sf.mzmine.parameters.ParameterSet;
import net.sf.mzmine.taskcontrol.Task;
import net.sf.mzmine.util.ExitCode;

/**
 * NIST MS Search module.
 */
public class NistMsSearchModule implements MZmineProcessingModule {

  private static final String MODULE_NAME = "NIST MS Search";
  private static final String MODULE_DESCRIPTION =
      "This method searches for spectra in the NIST library.";

  @Override
  public @Nonnull String getName() {

    return MODULE_NAME;
  }

  @Override
  public @Nonnull String getDescription() {

    return MODULE_DESCRIPTION;
  }

  @Override
  public @Nonnull MZmineModuleCategory getModuleCategory() {

    return MZmineModuleCategory.IDENTIFICATION;
  }

  @Override
  public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
    return NistMsSearchParameters.class;
  }

  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

    for (final PeakList peakList : parameters.getParameter(NistMsSearchParameters.PEAK_LISTS)
        .getValue().getMatchingPeakLists()) {

      tasks.add(new NistMsSearchTask(peakList, parameters));
    }

    return ExitCode.OK;
  }

  /**
   * Search for a peak-list row's mass spectrum.
   *
   * @param peakList the peak-list.
   * @param row the peak-list row.
   */
  public static void singleRowSearch(final PeakList peakList, final PeakListRow row) {

    final ParameterSet parameters =
        MZmineCore.getConfiguration().getModuleParameters(NistMsSearchModule.class);
    if (parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true) == ExitCode.OK) {

      MZmineCore.getTaskController().addTask(new NistMsSearchTask(row, peakList, parameters));
    }
  }
}
